cicd: update precommit (#227)

per
https://github.com/GenomicMedLab/software-templates/releases/tag/2025.01.08

Author: jsstevenson

.github/workflows/checks.yaml

@@ -68,7 +68,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        hook:
+        cmd:
           - "end-of-file-fixer"
           - "trailing-whitespace"
           - "mixed-line-ending"
@@ -82,7 +82,7 @@ jobs:
 
       - uses: pre-commit/[email protected]
         with:
-          extra_args: ${{ matrix.hook }} --all-files
+          extra_args: ${{ matrix.cmd }} --all-files
   docs:
     runs-on: ubuntu-latest
     env:

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.6.0  # pre-commit-hooks version
+  rev: v5.0.0  # pre-commit-hooks version
   hooks:
   - id: check-added-large-files
   - id: detect-private-key
@@ -17,4 +17,4 @@ repos:
     - id: ruff-format
     - id: ruff
       args: [ --fix, --exit-non-zero-on-fix ]
-minimum_pre_commit_version: 3.7.1
+minimum_pre_commit_version: 4.0.1

pyproject.toml

@@ -37,7 +37,12 @@ dynamic = ["version"]
 pg = ["psycopg[binary]", "requests"]
 etl = ["owlready2==0.40", "rdflib", "wags-tails>=0.1.2", "fastobo", "tqdm"]
 tests = ["pytest>=6.0", "pytest-cov", "httpx"]
-dev = ["pre-commit>=3.7.1", "ruff==0.8.6", "lxml", "xmlformatter"]
+dev = [
+    "pre-commit>=4.0.1",
+    "ruff==0.8.6",
+    "lxml",
+    "xmlformatter",
+]
 docs = [
     "sphinx==6.1.3",
     "sphinx-autodoc-typehints==1.22.0",